10x Xenium
Mouse hair follicle
GSM8546224
bronze Interactive viewer injury Provisional
print(sdata)
SpatialData object
├── Images
│ └── 'morphology_mip': DataArray[cyx] (1, 30589, 34173)
├── Labels
│ ├── 'cell_labels': DataTree[yx] (30589, 34173), (15294, 17086), (7647, 8543), (3823, 4271), (1911, 2135)
│ └── 'nucleus_labels': DataTree[yx] (30589, 34173), (15294, 17086), (7647, 8543), (3823, 4271), (1911, 2135)
├── Points
│ └── 'transcripts': DataFrame with shape: (8275955, 11) (3D points)
├── Shapes
│ ├── 'cell_boundaries': GeoDataFrame shape: (32760, 1) (2D shapes)
│ ├── 'cell_circles': GeoDataFrame shape: (32760, 2) (2D shapes)
│ └── 'nucleus_boundaries': GeoDataFrame shape: (32760, 2) (2D shapes)
└── Tables
└── 'table': AnnData (32760, 479)
with coordinate systems:
▸ 'global', with elements:
morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes) Load in Python
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("j6aTWbgoV2W3PdfV") # latest version
sdata = artifact.load() # cache, then load into memory
group = artifact.open() # stream without downloading
path = artifact.cache() # sync into the local cache, returns the path Load from the CLI
# one-shot: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/j6aTWbgoV2W3PdfV
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid j6aTWbgoV2W3PdfV Load with the Python client
# pip install git+https://github.com/theislab/spatialdata-db-client
from sddb import Catalog
ds = Catalog().cohort(uids=["j6aTWbgoV2W3PdfV0000"])[0]
ds.elements() # inspect without downloading
sdata = ds.load(lazy=False) # copy to the local cache and openPart of collection
In situ targeted gene expression analysis of healing skin on SD0 post-wounding in Wildtype and Rnasel knock out wounds→ 6 datasets · comparison
Metadata
- Technology
- 10x Xenium
- Organism
- mouse
- Tissue
- hair follicle
- Condition
- injury
- Modality
- RNA
- Observations
- 32,760
- Transcripts
- 8,275,955
- Tier
- bronze
- Size
- 689 MB
- Sample ID
- GSM8546224
- License
- NCBI GEO policy
- Published
- Feb 8, 2025
Cite this dataset
No linked publication found — please cite the data source: NCBI GEO ↗.
Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB